Package: Peptides 2.4.6

Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.

Authors:Daniel Osorio [aut, cre], Paola Rondon-Villarreal [aut, ths], Rodrigo Torres [aut, ths], J. Sebastian Paez [ctb], Luis Pedro Coelho [ctb], Richèl J.C. Bilderbeek [ctb], Florian C. Sigloch [ctb]

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Peptides/json (API)

# Install 'Peptides' in R:
install.packages('Peptides', repos = c('https://dosorio.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dosorio/peptides/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • AAdata - Properties, scales and indices for the 20 naturally occurring amino acids from various sources
  • pepdata - Physicochemical properties and indices from 100 amino acid sequences

On CRAN:

bioinformaticscalculate-indicespeptidesprotein-sequencesqsar

9.01 score 79 stars 7 packages 226 scripts 1.0k downloads 9 mentions 31 exports 1 dependencies

Last updated 12 months agofrom:a1a91be11b. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-win-x86_64OKNov 02 2024
R-4.5-linux-x86_64OKNov 02 2024
R-4.4-win-x86_64OKNov 02 2024
R-4.4-mac-x86_64OKNov 02 2024
R-4.4-mac-aarch64OKNov 02 2024
R-4.3-win-x86_64OKNov 02 2024
R-4.3-mac-x86_64OKNov 02 2024
R-4.3-mac-aarch64OKNov 02 2024

Exports:aaCompaaDescriptorsaaListaaSMILESaIndexautoCorrelationautoCovarianceblosumIndicesbomanchargecrossCovariancecrucianiPropertiesfasgaiVectorshmomenthydrophobicityinstaIndexkideraFactorslengthpepmassShiftmembposmswhimScoresmwmzpIplotXVGprotFPreadXVGstScalestScalesvhseScaleszScales

Dependencies:Rcpp

Readme and manuals

Help Manual

Help pageTopics
Compute the amino acid composition of a protein sequenceaaComp
Properties, scales and indices for the 20 naturally occurring amino acids from various sourcesAAdata
Compute 66 descriptors for each amino acid of a protein sequence.aaDescriptors
Return a vector with the 20 standard amino acids in upper caseaaList
Create Smiles String from aminoacid sequencesaaSMILES
Compute the aliphatic index of a protein sequenceaIndex
Compute the auto-correlation index of a protein sequenceautoCorrelation
Compute the auto-covariance index of a protein sequenceautoCovariance
Compute the BLOSUM62 derived indices of a protein sequenceblosumIndices
Compute the Boman (Potential Protein Interaction) indexboman
Compute the theoretical net charge of a protein sequencecharge
Compute the cross-covariance index of a protein sequencecrossCovariance
Compute the Cruciani properties of a protein sequencecrucianiProperties
Compute the FASGAI vectors of a protein sequencefasgaiVectors
Compute the hydrophobic moment of a protein sequencehmoment
Compute the hydrophobicity index of a protein sequencehydrophobicity
Compute the instability index of a protein sequenceinstaIndex
Compute the Kidera factors of a protein sequencekideraFactors
Compute the amino acid length of a protein sequencelengthpep
Calculate the mass difference of modified peptides.massShift
Compute theoretically the class of a protein sequencemembpos
Compute the MS-WHIM scores of a protein sequencemswhimScores
Compute the molecular weight of a protein sequencemw
Calculate the m/z for peptides.mz
Physicochemical properties and indices from 100 amino acid sequencespepdata
Compute the isoelectic point (pI) of a protein sequencepI
Plot time series from GROMACS XVG filesplotXVG
Compute the protFP descriptors of a protein sequenceprotFP
Read output data from a XVG format file.readXVG
Compute the ST-scales of a protein sequencestScales
Compute the T-scales of a protein sequencetScales
Compute the VHSE-scales of a protein sequencevhseScales
Compute the Z-scales of a protein sequencezScales